Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006565.1 Hibiscus syriacus cultivar Beakdansim tig00016066_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1014065
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:575725 original size:128 final size:128
Alignment explanation
Indices: 575483--575732 Score: 317
Period size: 128 Copynumber: 2.0 Consensus size: 128
575473 TGGTAACAAA
* *
575483 AAACGTCGCAATAGGTAACGATATATAGCGGCGTTTGTCCAACAAACGCCGCAATAGGTGTTGAT
1 AAACGCCGCAATAGGTAACGATATATAGCGGCGTTTGTCCAACAAACGCCGCAATAGGTCTTGAT
* * * * * * *
575548 ATTTGGTGGCTTTTTCCAACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCAAC
66 ATTTAGCGGCTTTTTCCAACAAACACCGCAAAAGATGCTGAGATATAGCGGCGTTTTTCCAAC
*** *
575611 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTGTCC-ACAAACGCCGCAATAGGTCTTGA
1 AAACGCCGCAATAGGTAACGATATATAGCGGCG-TTTGTCCAACAAACGCCGCAATAGGTCTTGA
* *
575675 TATTTAGCGGCGTTTTTCCTACAAACATCGCAAAAGAT-CTG-GTATATAGCGGCGTTTT
65 TATTTAGCGGC-TTTTTCCAACAAACACCGCAAAAGATGCTGAG-ATATAGCGGCGTTTT
575733 AAGATACAAA
Statistics
Matches: 104, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
127 1 0.01
128 75 0.72
129 28 0.27
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (128 bp):
AAACGCCGCAATAGGTAACGATATATAGCGGCGTTTGTCCAACAAACGCCGCAATAGGTCTTGAT
ATTTAGCGGCTTTTTCCAACAAACACCGCAAAAGATGCTGAGATATAGCGGCGTTTTTCCAAC
Found at i:575744 original size:86 final size:85
Alignment explanation
Indices: 575508--575732 Score: 240
Period size: 85 Copynumber: 2.6 Consensus size: 85
575498 TAACGATATA
* * * * * * * *
575508 TAGCGGCGTTTGTCCAACAAACGCCGCAATAGGTGTTGATATTTGGTGGC-TTTT-TCCAACAAA
1 TAGCGGCGTTTTTCCAACAAACACCGCAAAAGATGCTGATATATAGCGGCGTTTTGT-C-ACAAA
*
575571 CGCCGCAATAGGTGTTGAGATT
64 CGCCGCAATAGGTCTTGAGATT
* * * * *
575593 TAGCGGCGTTTTTCCAACAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTGTCCACAAAC
1 TAGCGGCGTTTTTCCAACAAACACCGCAAAAGATGCTGATATATAGCGGCGTTTTGT-CACAAAC
*
575658 GCCGCAATAGGTCTTGATATT
65 GCCGCAATAGGTCTTGAGATT
* * *
575679 TAGCGGCGTTTTTCCTACAAACATCGCAAAAGAT-CTGGTATATAGCGGCGTTTT
1 TAGCGGCGTTTTTCCAACAAACACCGCAAAAGATGCTGATATATAGCGGCGTTTT
575733 AAGATACAAA
Statistics
Matches: 125, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
85 64 0.51
86 58 0.46
87 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (85 bp):
TAGCGGCGTTTTTCCAACAAACACCGCAAAAGATGCTGATATATAGCGGCGTTTTGTCACAAACG
CCGCAATAGGTCTTGAGATT
Found at i:575886 original size:21 final size:21
Alignment explanation
Indices: 575873--575918 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
575863 CTTGACATCG
575873 ATAACAACAAACTTAAAATCC
1 ATAACAACAAACTTAAAATCC
* ** *
575894 ATAACAAGAAAAATGAAATCC
1 ATAACAACAAACTTAAAATCC
575915 ATAA
1 ATAA
575919 TAATAAATCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.61, C:0.17, G:0.04, T:0.17
Consensus pattern (21 bp):
ATAACAACAAACTTAAAATCC
Found at i:577939 original size:29 final size:29
Alignment explanation
Indices: 577899--577961 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
577889 TTCATTCAAC
577899 AGAAATGAAACCTAAAAATGGATTCAATG
1 AGAAATGAAACCTAAAAATGGATTCAATG
577928 AGAATATG-AACCTAAAAATGGATTCAATG
1 AGAA-ATGAAACCTAAAAATGGATTCAATG
577957 AGAAA
1 AGAAA
577962 AGATTAGGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
28 1 0.03
29 29 0.88
30 3 0.09
ACGTcount: A:0.52, C:0.10, G:0.17, T:0.21
Consensus pattern (29 bp):
AGAAATGAAACCTAAAAATGGATTCAATG
Found at i:580348 original size:42 final size:42
Alignment explanation
Indices: 580302--580706 Score: 441
Period size: 42 Copynumber: 9.8 Consensus size: 42
580292 TATGACAATT
580302 GCGGCGTTTGGTATTAAAACGCCACTAAAGTACGAGTCTATA
1 GCGGCGTTTGGTATTAAAACGCCACTAAAGTACGAGTCTATA
* * *
580344 GCGGCGTTTGTTATTAAAACGCCACAAAAGTACGTGTCTATA
1 GCGGCGTTTGGTATTAAAACGCCACTAAAGTACGAGTCTATA
* *
580386 GTGGCGTTTGTGTA--AAAACGCCACTAAAGTACGAATCTATA
1 GCGGCGTTTG-GTATTAAAACGCCACTAAAGTACGAGTCTATA
* * * * *
580427 GCGGCATTTGGGATTAAAACGCCACAAAAATACGTGTCTATA
1 GCGGCGTTTGGTATTAAAACGCCACTAAAGTACGAGTCTATA
* * * *
580469 GCGGCGTTTGGTATTAAAACACCACAAAAGTACGTGTCTATC
1 GCGGCGTTTGGTATTAAAACGCCACTAAAGTACGAGTCTATA
* *
580511 GCGGCGTTTGTGTA--AAAATGCCACTAAAGTATGAGTCTATA
1 GCGGCGTTTG-GTATTAAAACGCCACTAAAGTACGAGTCTATA
* * *
580552 GAGTCGTTTGGTATTAAAACGCCA-TAAAAGTACGTGTCTATA
1 GCGGCGTTTGGTATTAAAACGCCACT-AAAGTACGAGTCTATA
* * * * *
580594 GCAGCGTTT-GTATAAAAACGCCACTAAAATACTAGTTTATA
1 GCGGCGTTTGGTATTAAAACGCCACTAAAGTACGAGTCTATA
* * * * *
580635 GCGGCGTTT-GTATAAAAACGCCACTACATTACGATTCTTTA
1 GCGGCGTTTGGTATTAAAACGCCACTAAAGTACGAGTCTATA
*
580676 GCGGCGTTT-TTA-TACAAACGCCACTAAAGTA
1 GCGGCGTTTGGTATTA-AAACGCCACTAAAGTA
580707 TAGTATTTTG
Statistics
Matches: 304, Mismatches: 50, Indels: 19
0.82 0.13 0.05
Matches are distributed among these distances:
40 6 0.02
41 146 0.48
42 147 0.48
43 5 0.02
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (42 bp):
GCGGCGTTTGGTATTAAAACGCCACTAAAGTACGAGTCTATA
Found at i:580413 original size:83 final size:83
Alignment explanation
Indices: 580302--580706 Score: 425
Period size: 83 Copynumber: 4.9 Consensus size: 83
580292 TATGACAATT
580302 GCGGCGTTTGGTATTAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTTATTAAAACGCC
1 GCGGCGTTTGGTA-TAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTTATTAAAACGCC
580367 ACAAAAGTACGTGTCTATA
65 ACAAAAGTACGTGTCTATA
* * * **
580386 GTGGCGTTTGTGTA-AAAACGCCACTAAAGTACGAATCTATAGCGGCATTTGGGATTAAAACGCC
1 GCGGCGTTTG-GTATAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTTATTAAAACGCC
*
580450 ACAAAAATACGTGTCTATA
65 ACAAAAGTACGTGTCTATA
* * * * *
580469 GCGGCGTTTGGTATTAAAACACCACAAAAGTACGTGTCTATCGCGGCGTTTGTGTA--AAAATGC
1 GCGGCGTTTGGTA-TAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGT-TATTAAAACGC
* * *
580532 CACTAAAGTATGAGTCTATA
64 CACAAAAGTACGTGTCTATA
* * * * *
580552 GAGTCGTTTGGTATTAAAACGCCA-TAAAAGTACGTGTCTATAGCAGCGTTTG-TATAAAAACGC
1 GCGGCGTTTGGTA-TAAAACGCCACT-AAAGTACGAGTCTATAGCGGCGTTTGTTATTAAAACGC
*
580615 CACTAAAA-TAC-TAGTTTATA
64 CAC-AAAAGTACGT-GTCTATA
* * * *
580635 GCGGCGTTT-GTATAAAAACGCCACTACATTACGATTCTTTAGCGGCGTTT-TTA-TACAAACGC
1 GCGGCGTTTGGTAT-AAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTTATTA-AAACGC
*
580697 CACTAAAGTA
64 CACAAAAGTA
580707 TAGTATTTTG
Statistics
Matches: 266, Mismatches: 41, Indels: 30
0.79 0.12 0.09
Matches are distributed among these distances:
81 7 0.03
82 47 0.18
83 165 0.62
84 43 0.16
85 4 0.02
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (83 bp):
GCGGCGTTTGGTATAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTTATTAAAACGCCA
CAAAAGTACGTGTCTATA
Found at i:580446 original size:125 final size:124
Alignment explanation
Indices: 580302--580706 Score: 523
Period size: 125 Copynumber: 3.3 Consensus size: 124
580292 TATGACAATT
*
580302 GCGGCGTTTGGTATTAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTTATTAAAACGCC
1 GCGGCGTTTGGTATTAAAACGCCACTAAAGTACGTGTCTATAGCGGCGTTTG-TATTAAAACGCC
*
580367 ACAAAAGTACGTGTCTATAGTGGCGTTTGTGTAAAAACGCCACTAAAGTACGAATCTATA
65 ACAAAAGTACGTGTCTATAGCGGCGTTTGTGTAAAAACGCCACTAAAGTACGAATCTATA
* * * * *
580427 GCGGCATTTGGGATTAAAACGCCACAAAAATACGTGTCTATAGCGGCGTTTGGTATTAAAACACC
1 GCGGCGTTTGGTATTAAAACGCCACTAAAGTACGTGTCTATAGCGGCGTTT-GTATTAAAACGCC
* * * *
580492 ACAAAAGTACGTGTCTATCGCGGCGTTTGTGTAAAAATGCCACTAAAGTATGAGTCTATA
65 ACAAAAGTACGTGTCTATAGCGGCGTTTGTGTAAAAACGCCACTAAAGTACGAATCTATA
* * * *
580552 GAGTCGTTTGGTATTAAAACGCCA-TAAAAGTACGTGTCTATAGCAGCGTTTGTATAAAAACGCC
1 GCGGCGTTTGGTATTAAAACGCCACT-AAAGTACGTGTCTATAGCGGCGTTTGTATTAAAACGCC
* * * * * *
580616 ACTAAAA-TAC-TAGTTTATAGCGGCGTTTGTATAAAAACGCCACTACATTACGATTCTTTA
65 AC-AAAAGTACGT-GTCTATAGCGGCGTTTGTGTAAAAACGCCACTAAAGTACGAATCTATA
*
580676 GCGGCGTTT-TTA-TACAAACGCCACTAAAGTA
1 GCGGCGTTTGGTATTA-AAACGCCACTAAAGTA
580707 TAGTATTTTG
Statistics
Matches: 242, Mismatches: 32, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
122 2 0.01
123 17 0.07
124 63 0.26
125 159 0.66
126 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (124 bp):
GCGGCGTTTGGTATTAAAACGCCACTAAAGTACGTGTCTATAGCGGCGTTTGTATTAAAACGCCA
CAAAAGTACGTGTCTATAGCGGCGTTTGTGTAAAAACGCCACTAAAGTACGAATCTATA
Found at i:581038 original size:22 final size:21
Alignment explanation
Indices: 580993--581038 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
580983 CATTTTGGGA
*
580993 AAAAAGTATCGATACATATTT
1 AAAAAGTATCGATACATATGT
*
581014 AAAAAGTGTCGATACATAATGT
1 AAAAAGTATCGATACAT-ATGT
581036 AAA
1 AAA
581039 CCTATTTGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.50, C:0.09, G:0.13, T:0.28
Consensus pattern (21 bp):
AAAAAGTATCGATACATATGT
Found at i:581082 original size:20 final size:20
Alignment explanation
Indices: 581065--581103 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
581055 CCAGTATATT
581065 TTTACCGGTTACATTATAAA
1 TTTACCGGTTACATTATAAA
* *
581085 TTTACCTGTTACATAATAA
1 TTTACCGGTTACATTATAA
581104 TTATCGATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41
Consensus pattern (20 bp):
TTTACCGGTTACATTATAAA
Found at i:581680 original size:20 final size:20
Alignment explanation
Indices: 581631--581683 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
581621 CAGGTAGCGC
581631 TTTACCTG-TTTGTCATTTA
1 TTTACCTGTTTTGTCATTTA
** * *
581650 TAAACCGGTTTTGTCATTTT
1 TTTACCTGTTTTGTCATTTA
581670 TTTACCTGTTTTGT
1 TTTACCTGTTTTGT
581684 TATGGATCGA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.15, C:0.15, G:0.13, T:0.57
Consensus pattern (20 bp):
TTTACCTGTTTTGTCATTTA
Found at i:581942 original size:113 final size:112
Alignment explanation
Indices: 581594--582163 Score: 902
Period size: 112 Copynumber: 5.1 Consensus size: 112
581584 TCGATACTTA
* * * *
581594 TATAAAGTATCGACACTATCAACATATCAGGTAGCGCTTTACCTG-TTTGTCATTTATAAACCGG
1 TATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGG
581658 TTTTGTCATTTTTTTACCTG-T-T-TTGTTATGGATCGATACATTTT
66 TTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTT
* * * *
581702 TATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATATACCGA
1 TATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGG
* * *
581767 TTTTATCATTTTTTTAACTATTATATTGTTATGGATCGATACATTTT
66 TTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTT
*
581814 TATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTATCATTTATAGACCGG
1 TATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGG
581879 TTTTGTCATTTTTTTTACCTGTTATATTGTTATGGATCGATACATTTT
66 TTTTGTCA-TTTTTTTACCTGTTATATTGTTATGGATCGATACATTTT
* * *
581927 TATAGAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTATTTTTTCATTTATAGACCGG
1 TATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGG
* *
581992 TTTTGTCATTTTTTTACCTGTTATATTGTTATGGATAGATATATTTT
66 TTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTT
582039 TATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGG
1 TATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGG
* * *
582104 TTTTGTCA-TTTTTTACTTGTTATATTG-TATGGATCAATA-AATTT
66 TTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTT
582148 TATAAAGTATCGACAC
1 TATAAAGTATCGACAC
582164 AAACCGACAA
Statistics
Matches: 431, Mismatches: 26, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
108 44 0.10
109 54 0.13
110 11 0.03
111 19 0.04
112 196 0.45
113 107 0.25
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.45
Consensus pattern (112 bp):
TATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGG
TTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTT
Found at i:581983 original size:225 final size:224
Alignment explanation
Indices: 581594--582163 Score: 902
Period size: 225 Copynumber: 2.6 Consensus size: 224
581584 TCGATACTTA
* * * *
581594 TATAAAGTATCGACACTATCAACATATCAGGTAGCGCTTTACCTG-TTTGTCATTTATAAACCGG
1 TATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGG
581658 TTTTGTCATTTTTTTACCTG-T-T-TTGTTATGGATCGATACATTTTTATAAAGTATCGACACTA
66 TTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTA
* *
581720 TCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATATACCGATTTTATCATTTTTTTAAC
131 TCAACATATCCGGTAGCGCTTTACCTATTTTGTCATTTATAGACCGATTTTATCATTTTTTTAAC
*
581785 TATTATATTGTTATGGATCGATACATTTT
196 TATTATATTGTTATGGATAGATACATTTT
*
581814 TATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTATCATTTATAGACCGG
1 TATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGG
*
581879 TTTTGTCATTTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAGAGTATCGACACT
66 TTTTGTCA-TTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
* * * * * *
581944 TTCAATATATCCGGTAGCGCTTTACCTATTTTTTCATTTATAGACCGGTTTTGTCATTTTTTTAC
130 ATCAACATATCCGGTAGCGCTTTACCTATTTTGTCATTTATAGACCGATTTTATCATTTTTTTAA
* *
582009 CTGTTATATTGTTATGGATAGATATATTTT
195 CTATTATATTGTTATGGATAGATACATTTT
582039 TATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGG
1 TATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGG
* * *
582104 TTTTGTCA-TTTTTTACTTGTTATATTG-TATGGATCAATA-AATTTTATAAAGTATCGACAC
66 TTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACAC
582164 AAACCGACAA
Statistics
Matches: 323, Mismatches: 22, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
220 42 0.13
221 44 0.14
222 23 0.07
223 19 0.06
224 1 0.00
225 194 0.60
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.45
Consensus pattern (224 bp):
TATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGG
TTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTA
TCAACATATCCGGTAGCGCTTTACCTATTTTGTCATTTATAGACCGATTTTATCATTTTTTTAAC
TATTATATTGTTATGGATAGATACATTTT
Found at i:589594 original size:3 final size:3
Alignment explanation
Indices: 589586--589665 Score: 160
Period size: 3 Copynumber: 26.7 Consensus size: 3
589576 GGTTAAAGAT
589586 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC
589634 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
589666 ACAAAGAAGA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (3 bp):
TCC
Found at i:591472 original size:228 final size:227
Alignment explanation
Indices: 591060--591507 Score: 781
Period size: 229 Copynumber: 2.0 Consensus size: 227
591050 GTAAATTATC
* * *
591060 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
**
591125 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
*
591190 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATTG
591255 AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAACATAAATTACATAACTTT-AAAAAAGTATA
*
591288 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
591353 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
* *
591418 TTGTGTAAATTAAATTATT-AATTAATATTGTAGGTGGAAAACATAAAACACTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATT
591482 GAAACATAAATTACATAACTTTAAAA
195 GAAACATAAATTACATAACTTTAAAA
591508 GCAGTTTTAA
Statistics
Matches: 209, Mismatches: 10, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
227 4 0.02
228 101 0.48
229 104 0.50
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:591596 original size:20 final size:20
Alignment explanation
Indices: 591573--591622 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
591563 CGATATACCA
591573 GGTAAAATTATGATAAAACC
1 GGTAAAATTATGATAAAACC
*
591593 GGTAACAA-AATGATAAAACC
1 GGTAA-AATTATGATAAAACC
591613 GGTAAAATTA
1 GGTAAAATTA
591623 AAAGTGTCGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.52, C:0.10, G:0.16, T:0.22
Consensus pattern (20 bp):
GGTAAAATTATGATAAAACC
Found at i:591763 original size:20 final size:20
Alignment explanation
Indices: 591740--591787 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
591730 CGATATAACA
*
591740 GGTAAAAATATGAT-AAAACC
1 GGTAAAAA-ATGATAAAAAAC
*
591760 GGTATCAAAATGATAAAAAAC
1 GGTA-AAAAATGATAAAAAAC
591781 GGTAAAA
1 GGTAAAA
591788 TGATACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.56, C:0.08, G:0.17, T:0.19
Consensus pattern (20 bp):
GGTAAAAAATGATAAAAAAC
Found at i:593913 original size:19 final size:19
Alignment explanation
Indices: 593850--593912 Score: 110
Period size: 19 Copynumber: 3.4 Consensus size: 19
593840 AATGTCGAGT
*
593850 TAATTTTGTATAAGATTTA
1 TAATTTTGTATACGATTTA
593869 TAATTTTGTATACGATTTA
1 TAATTTTGTATACGATTTA
593888 TAATTTTGTATACGATTTA
1 TAATTTTGTATACGATTTA
593907 T-ATTTT
1 TAATTTT
593913 TTTATGTGAA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
18 5 0.12
19 38 0.88
ACGTcount: A:0.32, C:0.03, G:0.10, T:0.56
Consensus pattern (19 bp):
TAATTTTGTATACGATTTA
Found at i:594530 original size:198 final size:199
Alignment explanation
Indices: 593989--595203 Score: 2144
Period size: 198 Copynumber: 6.1 Consensus size: 199
593979 TTAAGGGTCA
* * ** *
593989 TGTCGATACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATT-TTACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAACAAGGTGCACCA
594053 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
594118 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
594183 AATG
196 AATG
594187 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAA-ACAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAACA-AGGTGCACC
*
594251 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
65 AATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
594316 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
130 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
594381 TAATG
195 TAATG
*
594386 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTCCCAGAATGAATTAAAACAAGGTGCACCC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAACAAGGTGCACCA
594450 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
594515 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
594580 AATG
196 AATG
*** *
594584 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAATGAATTTTTACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAACAAGGTGCACCA
594648 ATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
594712 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
594777 AATG
196 AATG
594781 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATT-AAAACAAGGTGCACC
*
594845 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
65 AATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
594910 GTAATATGTAATTTTTTAATCTAACCGGTAC-ATTATACCGGTTTTATGAGAGAATAAGTCTAAA
130 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
594974 TAATG
195 TAATG
* *** * *
594979 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGAATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAACAAGGTGCACCA
595044 ATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
595108 TAATATGTAATTTTT-AATCTAACCGGTACAATTATACCGG-TTTATGAGAGAATATGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
595171 AATG
196 AATG
*
595175 TGTCGACACTAATATATTTTGTGTCGATA
1 TGTCGACACTAATATAGTTTGTGTCGATA
595204 CTAATTTAAA
Statistics
Matches: 981, Mismatches: 27, Indels: 20
0.95 0.03 0.02
Matches are distributed among these distances:
196 74 0.08
197 221 0.23
198 418 0.43
199 268 0.27
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (199 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAACAAGGTGCACCA
ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
AATG
Found at i:596684 original size:18 final size:18
Alignment explanation
Indices: 596661--596722 Score: 88
Period size: 18 Copynumber: 3.4 Consensus size: 18
596651 ATCGGTCGCA
* * *
596661 GAAGATGAAGCTGACGAT
1 GAAGATGACGATGATGAT
596679 GAAGATGACGATGATGAT
1 GAAGATGACGATGATGAT
*
596697 GATGATGACGATGATGAT
1 GAAGATGACGATGATGAT
596715 GAAGATGA
1 GAAGATGA
596723 TGATCCAAAC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.39, C:0.06, G:0.34, T:0.21
Consensus pattern (18 bp):
GAAGATGACGATGATGAT
Found at i:596685 original size:6 final size:6
Alignment explanation
Indices: 596661--596722 Score: 61
Period size: 6 Copynumber: 10.3 Consensus size: 6
596651 ATCGGTCGCA
* * * * * *
596661 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GATGAT GACGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
*
596709 GATGAT GAAGAT GA
1 GAAGAT GAAGAT GA
596723 TGATCCAAAC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.39, C:0.06, G:0.34, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:596696 original size:3 final size:3
Alignment explanation
Indices: 596676--596726 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
596666 TGAAGCTGAC
* * * *
596676 GAT GAA GAT GAC GAT GAT GAT GAT GAT GAC GAT GAT GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
596724 GAT
1 GAT
596727 CCAAACAAGT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.37, C:0.04, G:0.33, T:0.25
Consensus pattern (3 bp):
GAT
Found at i:596723 original size:12 final size:12
Alignment explanation
Indices: 596664--596726 Score: 81
Period size: 12 Copynumber: 5.2 Consensus size: 12
596654 GGTCGCAGAA
* *
596664 GATGAAGCTGAC
1 GATGAAGATGAT
*
596676 GATGAAGATGAC
1 GATGAAGATGAT
*
596688 GATGATGATGAT
1 GATGAAGATGAT
*
596700 GATGACGATGAT
1 GATGAAGATGAT
596712 GATGAAGATGAT
1 GATGAAGATGAT
596724 GAT
1 GAT
596727 CCAAACAAGT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 46 1.00
ACGTcount: A:0.37, C:0.06, G:0.33, T:0.24
Consensus pattern (12 bp):
GATGAAGATGAT
Found at i:596940 original size:23 final size:23
Alignment explanation
Indices: 596909--596971 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
596899 ATAGGTAAAC
*
596909 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
596932 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
596955 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
596972 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:596979 original size:23 final size:23
Alignment explanation
Indices: 596909--596981 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
596899 ATAGGTAAAC
* * **
596909 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
596932 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
596955 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
596978 ATAT
1 ATAT
596982 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:597370 original size:23 final size:23
Alignment explanation
Indices: 597339--597401 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
597329 ATAGGTAAAC
*
597339 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
597362 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
597385 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
597402 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:597409 original size:23 final size:23
Alignment explanation
Indices: 597339--597411 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
597329 ATAGGTAAAC
* * **
597339 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
597362 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
597385 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
597408 ATAT
1 ATAT
597412 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:597662 original size:430 final size:430
Alignment explanation
Indices: 596803--597680 Score: 1740
Period size: 430 Copynumber: 2.0 Consensus size: 430
596793 GTCCTTGCCT
596803 ACATGAAACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCT
1 ACATGAAACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCT
596868 TTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTA
66 TTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTA
596933 TATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCC
131 TATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCC
596998 TTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGT
196 TTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGT
597063 GAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATA
261 GAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATA
597128 TATTATTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTT
326 TATTATTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTT
597193 TTGTGCAAATGAAATTATTAAATCAATATTGTAGTGGAAA
391 TTGTGCAAATGAAATTATTAAATCAATATTGTAGTGGAAA
597233 ACATGAAACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCT
1 ACATGAAACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCT
597298 TTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTA
66 TTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTA
597363 TATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCC
131 TATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCC
597428 TTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGT
196 TTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGT
597493 GAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTA-TTTTTACGTTACGGTATA
261 GAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATA
597557 TATTATTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTT
326 TATTATTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTT
597622 TTGTGCAAATGAAATTATTAAATCAATATTGTAGGTGGAAA
391 TTGTGCAAATGAAATTATTAAATCAATATTGTA-GTGGAAA
597663 ACATGAAACACTGTTAAA
1 ACATGAAACACTGTTAAA
597681 GTATCGATCC
Statistics
Matches: 447, Mismatches: 0, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
429 116 0.26
430 331 0.74
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.39
Consensus pattern (430 bp):
ACATGAAACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCT
TTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTA
TATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCC
TTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGT
GAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATA
TATTATTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTT
TTGTGCAAATGAAATTATTAAATCAATATTGTAGTGGAAA
Found at i:598773 original size:20 final size:21
Alignment explanation
Indices: 598734--598774 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
598724 CGAGTTAATC
*
598734 CGTTGATCAGGACACGTTGAT
1 CGTTGATCAGAACACGTTGAT
*
598755 CGTTGATCA-AACACTTTGAT
1 CGTTGATCAGAACACGTTGAT
598775 TTTGACCACG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.32
Consensus pattern (21 bp):
CGTTGATCAGAACACGTTGAT
Found at i:599265 original size:2 final size:2
Alignment explanation
Indices: 599258--599291 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
599248 TCTATTTTTA
*
599258 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
599292 CTGAACTATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:601088 original size:26 final size:26
Alignment explanation
Indices: 601037--601098 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
601027 TATTATTAAA
*
601037 ATAAGAATATAATAGTATCATATATT
1 ATAATAATATAATAGTATCATATATT
*
601063 ATTATAATATAATTGAGTAT-AT-TATT
1 ATAATAATATAA-T-AGTATCATATATT
*
601089 GTAATAATAT
1 ATAATAATAT
601099 TATTATTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
26 22 0.73
27 3 0.10
28 5 0.17
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.44
Consensus pattern (26 bp):
ATAATAATATAATAGTATCATATATT
Found at i:601104 original size:17 final size:17
Alignment explanation
Indices: 601082--601148 Score: 77
Period size: 17 Copynumber: 4.1 Consensus size: 17
601072 TAATTGAGTA
*
601082 TATTATTGTAATAATAT
1 TATTATTATAATAATAT
*
601099 TATTATTATAATAATAA
1 TATTATTATAATAATAT
*
601116 TATTATTAT-ATTATAT
1 TATTATTATAATAATAT
*
601132 TATTA--ATAATATTAT
1 TATTATTATAATAATAT
601147 TA
1 TA
601149 AAAATATTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
14 2 0.05
15 7 0.16
16 10 0.23
17 24 0.56
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (17 bp):
TATTATTATAATAATAT
Found at i:601105 original size:20 final size:20
Alignment explanation
Indices: 601059--601195 Score: 79
Period size: 20 Copynumber: 6.8 Consensus size: 20
601049 TAGTATCATA
601059 TATTATTATAAT-ATAAT-T
1 TATTATTATAATAATAATAT
* **
601077 GAGTATATTATTGTAATAATAT
1 TA-T-TATTATAATAATAATAT
601099 TATTATTATAATAATAATAT
1 TATTATTATAATAATAATAT
* * *
601119 TATTATATTATATTATTAATAA
1 TA-T-TATTATAATAATAATAT
*
601141 TATTATTA-AA-AAT-ATTT
1 TATTATTATAATAATAATAT
*
601158 TAAATATGT-TAATAATTAATAT
1 T-ATTAT-TATAATAA-TAATAT
* *
601180 TTTTATTAAAATAATA
1 TATTATTATAATAATA
601196 CTAAATATTA
Statistics
Matches: 88, Mismatches: 18, Indels: 24
0.68 0.14 0.18
Matches are distributed among these distances:
17 3 0.03
18 7 0.08
19 5 0.06
20 34 0.39
21 17 0.19
22 22 0.25
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
TATTATTATAATAATAATAT
Found at i:601138 original size:28 final size:28
Alignment explanation
Indices: 601095--601148 Score: 87
Period size: 25 Copynumber: 2.0 Consensus size: 28
601085 TATTGTAATA
601095 ATATTATTATTATAATAATAATATTATT
1 ATATTATTATTATAATAATAATATTATT
601123 ATATTA-TATTAT--TAATAATATTATT
1 ATATTATTATTATAATAATAATATTATT
601148 A
1 A
601149 AAAATATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
25 14 0.54
27 6 0.23
28 6 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
ATATTATTATTATAATAATAATATTATT
Found at i:601212 original size:18 final size:17
Alignment explanation
Indices: 601191--601224 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
601181 TTTATTAAAA
601191 TAATACTAAATATTATAT
1 TAATACTAAAT-TTATAT
*
601209 TAATATTAAATTTATA
1 TAATACTAAATTTATA
601225 AAATAATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATACTAAATTTATAT
Found at i:603458 original size:24 final size:24
Alignment explanation
Indices: 603431--603478 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
603421 GTTTAAGTCC
*
603431 CACTATGTCTACTGTAGAGGAAAT
1 CACTATGTCTACCGTAGAGGAAAT
603455 CACTATGTCTACCGTAGAGGAAAT
1 CACTATGTCTACCGTAGAGGAAAT
603479 TGATTAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (24 bp):
CACTATGTCTACCGTAGAGGAAAT
Found at i:603831 original size:14 final size:14
Alignment explanation
Indices: 603793--603833 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
603783 ATTTTTTGAT
603793 TTTTTAAAAAAATA
1 TTTTTAAAAAAATA
**
603807 TTTTTTTAAAAATA
1 TTTTTAAAAAAATA
603821 TTTTTAAAAAAAT
1 TTTTTAAAAAAAT
603834 CTAAACGTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TTTTTAAAAAAATA
Found at i:604097 original size:2 final size:2
Alignment explanation
Indices: 604090--604114 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
604080 GATGTTTTAC
604090 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
604115 AAAGATGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:604326 original size:113 final size:113
Alignment explanation
Indices: 604128--604351 Score: 412
Period size: 113 Copynumber: 2.0 Consensus size: 113
604118 GATGATTCAC
*
604128 TTACATTATATAAAATTAATAAGTTTTAAATTAATCTATATCTATTAGATTTAAATAAATAAGTA
1 TTACATTATATAAAATTAATAAGTTTTAAATTAATCTATAGCTATTAGATTTAAATAAATAAGTA
*
604193 GCTTATATTTAATTAAAATTTACAATCCATAAATGAACATCTTTTAGT
66 GCTTATATTTAATTAAAATTTACAATCCACAAATGAACATCTTTTAGT
*
604241 TTACATTATGTAAAATTAATAAGTTTTAAATTAATCTATAGCTATTAGATTTAAATAAATAAGTA
1 TTACATTATATAAAATTAATAAGTTTTAAATTAATCTATAGCTATTAGATTTAAATAAATAAGTA
*
604306 GCTTATATTTAATTAAAATTTACAATCCACAAATGAATATCTTTTA
66 GCTTATATTTAATTAAAATTTACAATCCACAAATGAACATCTTTTA
604352 ACTCATAGTA
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
113 107 1.00
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (113 bp):
TTACATTATATAAAATTAATAAGTTTTAAATTAATCTATAGCTATTAGATTTAAATAAATAAGTA
GCTTATATTTAATTAAAATTTACAATCCACAAATGAACATCTTTTAGT
Found at i:604464 original size:14 final size:14
Alignment explanation
Indices: 604435--604532 Score: 87
Period size: 14 Copynumber: 7.1 Consensus size: 14
604425 CTAAACCCCT
* *
604435 ATCTTAAACCCCAA
1 ATCTTAAATCCTAA
*
604449 ATCTTAAATTCTAA
1 ATCTTAAATCCTAA
*
604463 AT-TTCAAATCCCAA
1 ATCTT-AAATCCTAA
* *
604477 ATTTTAAATCTTAA
1 ATCTTAAATCCTAA
604491 A-CTATAAATCCTAA
1 ATCT-TAAATCCTAA
604505 ATCTTAAA-CCTTAA
1 ATCTTAAATCC-TAA
604519 A-CTTAAATCCTAA
1 ATCTTAAATCCTAA
604532 A
1 A
604533 CTGTAATCTT
Statistics
Matches: 69, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
13 15 0.22
14 50 0.72
15 4 0.06
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (14 bp):
ATCTTAAATCCTAA
Found at i:604490 original size:7 final size:7
Alignment explanation
Indices: 604447--604545 Score: 66
Period size: 7 Copynumber: 14.4 Consensus size: 7
604437 CTTAAACCCC
604447 AAATCTT
1 AAATCTT
604454 AAAT-TCT
1 AAATCT-T
604461 AAAT-TT
1 AAATCTT
**
604467 CAAATCCC
1 -AAATCTT
*
604475 AAATTTT
1 AAATCTT
604482 AAATCTT
1 AAATCTT
604489 AAA-CTAT
1 AAATCT-T
*
604496 AAATCCT
1 AAATCTT
604503 AAATCTT
1 AAATCTT
*
604510 AAACCTT
1 AAATCTT
604517 AAA-CTT
1 AAATCTT
*
604523 AAATCCT
1 AAATCTT
604530 AAA-CTGT
1 AAATCT-T
604537 -AATCTT
1 AAATCTT
604543 AAA
1 AAA
604546 AAATCTTTTT
Statistics
Matches: 72, Mismatches: 11, Indels: 18
0.71 0.11 0.18
Matches are distributed among these distances:
6 14 0.19
7 57 0.79
8 1 0.01
ACGTcount: A:0.45, C:0.18, G:0.01, T:0.35
Consensus pattern (7 bp):
AAATCTT
Found at i:604545 original size:13 final size:13
Alignment explanation
Indices: 604480--604545 Score: 71
Period size: 13 Copynumber: 4.9 Consensus size: 13
604470 ATCCCAAATT
604480 TTAAATCTTAAAC
1 TTAAATCTTAAAC
*
604493 TATAAATCCTAAATC
1 T-TAAATCTTAAA-C
*
604508 TTAAACCTTAAAC
1 TTAAATCTTAAAC
*
604521 TTAAATCCTAAAC
1 TTAAATCTTAAAC
604534 TGT-AATCTTAAA
1 T-TAAATCTTAAA
604546 AAATCTTTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
13 22 0.50
14 20 0.45
15 2 0.05
ACGTcount: A:0.45, C:0.18, G:0.02, T:0.35
Consensus pattern (13 bp):
TTAAATCTTAAAC
Found at i:605771 original size:19 final size:18
Alignment explanation
Indices: 605738--605773 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
605728 CCACAAGCAC
605738 ATATGTAGGAATTATGAT
1 ATATGTAGGAATTATGAT
*
605756 ATATGTTAGGATTTATGA
1 ATATG-TAGGAATTATGA
605774 AGCTCGATCG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.36, C:0.00, G:0.22, T:0.42
Consensus pattern (18 bp):
ATATGTAGGAATTATGAT
Found at i:606401 original size:20 final size:20
Alignment explanation
Indices: 606388--606432 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
606378 AAACTTTAGG
606388 GAAAGTTTCGAAACTCTTGA
1 GAAAGTTTCGAAACTCTTGA
*
606408 GATAGTTTCGAAACTCTTGA
1 GAAAGTTTCGAAACTCTTGA
606428 -AAAGT
1 GAAAGT
606433 ATCAAAAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (20 bp):
GAAAGTTTCGAAACTCTTGA
Found at i:608283 original size:16 final size:17
Alignment explanation
Indices: 608257--608288 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
608247 GGCAACATCT
608257 TTTTCTTTCTTTTCTTG
1 TTTTCTTTCTTTTCTTG
608274 TTTT-TTTCTTTTCTT
1 TTTTCTTTCTTTTCTT
608289 CTTGTTCTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (17 bp):
TTTTCTTTCTTTTCTTG
Found at i:608290 original size:19 final size:20
Alignment explanation
Indices: 608256--608294 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
608246 AGGCAACATC
*
608256 TTTTTCTTTCTTTTCTTGTT
1 TTTTTCTTTCTCTTCTTGTT
608276 TTTTTCTTT-TCTTCTTGTT
1 TTTTTCTTTCTCTTCTTGTT
608295 CTTGTTCCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.79
Consensus pattern (20 bp):
TTTTTCTTTCTCTTCTTGTT
Found at i:608306 original size:25 final size:25
Alignment explanation
Indices: 608257--608306 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
608247 GGCAACATCT
**
608257 TTTTCTTTCTTTTCTTGTTTTTTTC
1 TTTTCTTTCTTTTCTTGTTCCTTTC
608282 TTTTC-TTCTTGTTCTTGTTCCTTTC
1 TTTTCTTTCTT-TTCTTGTTCCTTTC
608307 CATTATCTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.00, C:0.20, G:0.06, T:0.74
Consensus pattern (25 bp):
TTTTCTTTCTTTTCTTGTTCCTTTC
Found at i:610322 original size:101 final size:103
Alignment explanation
Indices: 610135--610336 Score: 291
Period size: 101 Copynumber: 2.0 Consensus size: 103
610125 CAAGTACTTT
* * * * *
610135 GGGTGAGTCCTAAATCACCGTTAACATCAAGAATGTATACCCAACTAATCTACTCCGTTCTAATA
1 GGGTGAGTCCTAAATCACCGTTAACATCAAGAATGTACACCCAACTAATATACTCCGCTCGAACA
610200 TTTTAGATCATATAACGTTAG-AAAAACATTCAACTGG
66 TTTTAGATCATATAACGTTAGAAAAAACATTCAACTGG
* * * * * *
610237 GGGTGAGT-CTGAATCACCGTTAAGATCAAGAATGTACACTCGACTAGTATACTCCGCTCGAGCA
1 GGGTGAGTCCTAAATCACCGTTAACATCAAGAATGTACACCCAACTAATATACTCCGCTCGAACA
610301 TTTTAGATCATATAACGTTAGAAAAAACATTCAACT
66 TTTTAGATCATATAACGTTAGAAAAAACATTCAACT
610337 TACATTTTCA
Statistics
Matches: 88, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
101 66 0.75
102 22 0.25
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (103 bp):
GGGTGAGTCCTAAATCACCGTTAACATCAAGAATGTACACCCAACTAATATACTCCGCTCGAACA
TTTTAGATCATATAACGTTAGAAAAAACATTCAACTGG
Found at i:612092 original size:20 final size:20
Alignment explanation
Indices: 612043--612098 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
612033 TGATATTGAC
* *
612043 CCTTCAGTATCGATATTAAA
1 CCTTTAGTATCGATACTAAA
612063 CCTTTAGTATCGATACT-AA
1 CCTTTAGTATCGATACTAAA
*
612082 CCTGTTGGTATCGATAC
1 CCT-TTAGTATCGATAC
612099 CCTCACTGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 5 0.16
20 27 0.84
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (20 bp):
CCTTTAGTATCGATACTAAA
Found at i:616442 original size:24 final size:24
Alignment explanation
Indices: 616410--616456 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
616400 AGTCTTGCTG
616410 ATGATGTATAAAACATCTATGTAT
1 ATGATGTATAAAACATCTATGTAT
616434 ATGATGTATAAAACATCTATGTA
1 ATGATGTATAAAACATCTATGTA
616457 CAATTTCATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.36
Consensus pattern (24 bp):
ATGATGTATAAAACATCTATGTAT
Found at i:617825 original size:31 final size:31
Alignment explanation
Indices: 617749--617826 Score: 147
Period size: 31 Copynumber: 2.5 Consensus size: 31
617739 AATTACCATT
*
617749 AAACCAAGACACCTAAACCTTATCATCTTCC
1 AAACCAAGACACCTCAACCTTATCATCTTCC
617780 AAACCAAGACACCTCAACCTTATCATCTTCC
1 AAACCAAGACACCTCAACCTTATCATCTTCC
617811 AAACCAAGACACCTCA
1 AAACCAAGACACCTCA
617827 GACACTTCAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.40, C:0.37, G:0.04, T:0.19
Consensus pattern (31 bp):
AAACCAAGACACCTCAACCTTATCATCTTCC
Found at i:618286 original size:29 final size:30
Alignment explanation
Indices: 618202--618288 Score: 88
Period size: 30 Copynumber: 2.9 Consensus size: 30
618192 AATTTGAATT
* * * *
618202 TTTTTAAAATTATCATATTGGTCCCTAAAC
1 TTTTCAAAATTTTCATTTTGGTCACTAAAC
* *
618232 TTTTTAAAAGTTTAT-ACTTTGGTCACTAAAC
1 TTTTCAAAA-TTT-TCATTTTGGTCACTAAAC
618263 -TTTCAAAATTTTCATTTTGGTCACTA
1 TTTTCAAAATTTTCATTTTGGTCACTA
618289 TCTAAATTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
28 1 0.02
29 15 0.31
30 16 0.33
31 15 0.31
32 1 0.02
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (30 bp):
TTTTCAAAATTTTCATTTTGGTCACTAAAC
Found at i:623982 original size:24 final size:25
Alignment explanation
Indices: 623948--623994 Score: 87
Period size: 24 Copynumber: 1.9 Consensus size: 25
623938 CAAGTCTTGC
623948 TGATGATATAAAACATCTATGTATA
1 TGATGATATAAAACATCTATGTATA
623973 TGATG-TATAAAACATCTATGTA
1 TGATGATATAAAACATCTATGTA
623995 CAATTTCATG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.36
Consensus pattern (25 bp):
TGATGATATAAAACATCTATGTATA
Found at i:624837 original size:31 final size:31
Alignment explanation
Indices: 624787--624849 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
624777 AATTACCATT
*
624787 AAACAAAGACTCCTAAACCTTATCATTTTCC
1 AAACAAAGACACCTAAACCTTATCATTTTCC
* *
624818 AAACCAAGACACCTCAACCTTATCATTTTCC
1 AAACAAAGACACCTAAACCTTATCATTTTCC
624849 A
1 A
624850 TAAGTCAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.38, C:0.32, G:0.03, T:0.27
Consensus pattern (31 bp):
AAACAAAGACACCTAAACCTTATCATTTTCC
Found at i:634572 original size:16 final size:16
Alignment explanation
Indices: 634553--634583 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
634543 AATAAAAATC
634553 TATAAAATTAAATCGA
1 TATAAAATTAAATCGA
634569 TATAAAATTAAATCG
1 TATAAAATTAAATCG
634584 TACTCCCATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.32
Consensus pattern (16 bp):
TATAAAATTAAATCGA
Found at i:645666 original size:12 final size:12
Alignment explanation
Indices: 645649--645684 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
645639 GTATAACAAC
*
645649 TTTCCAAGCATA
1 TTTCCAAGCACA
645661 TTTCCAAGCACA
1 TTTCCAAGCACA
645673 TTTCCAAGCACA
1 TTTCCAAGCACA
645685 AAGCCCTCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.33, C:0.31, G:0.08, T:0.28
Consensus pattern (12 bp):
TTTCCAAGCACA
Found at i:648725 original size:30 final size:31
Alignment explanation
Indices: 648700--648763 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 31
648690 TTAAGTAAAT
*
648700 TACTTAGTGTTCGAGAGAAACTAAGTTAAGGA
1 TACTTAGTGCTCGAGAGAAACTAAGTTAA-GA
* * *
648732 TCCTTAGTGCTCGAGAGAAACTAGGTGAAGA
1 TACTTAGTGCTCGAGAGAAACTAAGTTAAGA
648763 T
1 T
648764 CAACGTGTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 3 0.11
32 25 0.89
ACGTcount: A:0.34, C:0.12, G:0.27, T:0.27
Consensus pattern (31 bp):
TACTTAGTGCTCGAGAGAAACTAAGTTAAGA
Found at i:658382 original size:5 final size:5
Alignment explanation
Indices: 658372--658581 Score: 420
Period size: 5 Copynumber: 42.0 Consensus size: 5
658362 TTAAAGTTAC
658372 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
658422 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
658472 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
658522 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
658572 TATAA TATAA
1 TATAA TATAA
658582 GGTAAACTAC
Statistics
Matches: 205, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 205 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:665733 original size:42 final size:42
Alignment explanation
Indices: 665674--665758 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
665664 ATTTACGTAG
665674 CTTACCTTGTAGTATAATATGCGACTAAATCTATAACTTACA
1 CTTACCTTGTAGTATAATATGCGACTAAATCTATAACTTACA
*
665716 CTTACCTTGTAGTATAATATGTGACTAAATCTATAACTTACA
1 CTTACCTTGTAGTATAATATGCGACTAAATCTATAACTTACA
665758 C
1 C
665759 GTAGTATATA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.36
Consensus pattern (42 bp):
CTTACCTTGTAGTATAATATGCGACTAAATCTATAACTTACA
Found at i:673422 original size:23 final size:22
Alignment explanation
Indices: 673396--673459 Score: 56
Period size: 23 Copynumber: 2.8 Consensus size: 22
673386 CAGCTCATAT
673396 AATTGCACCTAAGTGCCACGTAA
1 AATTGCACCT-AGTGCCACGTAA
* * * * *
673419 AATTGAACCGGAGTGTCGCGTAG
1 AATTGCACC-TAGTGCCACGTAA
673442 AATTGCACCGTAGTGCCA
1 AATTGCACC-TAGTGCCA
673460 TATAATAATG
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.30, C:0.23, G:0.25, T:0.22
Consensus pattern (22 bp):
AATTGCACCTAGTGCCACGTAA
Found at i:673680 original size:99 final size:102
Alignment explanation
Indices: 673475--673788 Score: 514
Period size: 100 Copynumber: 3.1 Consensus size: 102
673465 TAATGTCCAT
*
673475 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATATGTCTCACCA
1 AAGGACCACATATCATT-CTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
673540 GACTTCACACATGTTCCAAAGAATACATATATGTCTCG
65 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
673578 AAGGACCACATAACA-T-TTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCA-CAG
1 AAGGACCACATATCATTCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAG
*
673640 ACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 ACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
673677 AAGGACCACATATCATTCCTTAAGAATC--ATACATATGCCAAGGTTCAAGTATG-GTCTCACCA
1 AAGGACCACATATCATT-CTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
673739 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
65 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
673777 AAGGACCACATA
1 AAGGACCACATA
673789 GACCTCTACC
Statistics
Matches: 198, Mismatches: 9, Indels: 11
0.91 0.04 0.05
Matches are distributed among these distances:
99 58 0.29
100 116 0.59
102 10 0.05
103 14 0.07
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (102 bp):
AAGGACCACATATCATTCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAG
ACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:674287 original size:18 final size:18
Alignment explanation
Indices: 674264--674300 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
674254 TTTTTTATTA
*
674264 TGGGGGAATCGGTTCCCC
1 TGGGGGAATCGATTCCCC
*
674282 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
674300 T
1 T
674301 CTAGCGTTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.27, G:0.35, T:0.27
Consensus pattern (18 bp):
TGGGGGAATCGATTCCCC
Found at i:680397 original size:23 final size:23
Alignment explanation
Indices: 680371--680423 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
680361 CAGCTCATAT
*
680371 AATTGCACCTAAGTGCCACGTAA
1 AATTGCACCGAAGTGCCACGTAA
* * *
680394 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAA
680417 AATTGCA
1 AATTGCA
680424 TAGTAGTGCC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.21
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAA
Found at i:680431 original size:23 final size:23
Alignment explanation
Indices: 680382--680434 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
680372 ATTGCACCTA
*
680382 AGTGCCACGTAAAATTGCACCGG
1 AGTGCCACGTAAAATTGCACAGG
* * * *
680405 AGTGCCGCGTAGAATTGCATAGT
1 AGTGCCACGTAAAATTGCACAGG
680428 AGTGCCA
1 AGTGCCA
680435 TATAATAATG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.21
Consensus pattern (23 bp):
AGTGCCACGTAAAATTGCACAGG
Found at i:680626 original size:103 final size:103
Alignment explanation
Indices: 680450--680768 Score: 579
Period size: 103 Copynumber: 3.1 Consensus size: 103
680440 TAATGTCCAT
*
680450 AAGGACCACATATCATTCCTTAAGAATCATATACATATTCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
680515 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
680553 AAGGACCACATATCATTCCTTAATAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
* * *
680618 GACCTCACACATGTTCTAAAGAATACATATATGTCTCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
680656 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
680721 GACTTCACACATGTTCCAAAGAATAC--ATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
680757 AAGGACCACATA
1 AAGGACCACATA
680769 GACCCTCTAC
Statistics
Matches: 207, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
101 21 0.10
103 186 0.90
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:681284 original size:19 final size:20
Alignment explanation
Indices: 681247--681284 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
681237 TTTTTTATTA
*
681247 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
681267 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
681285 TCTAGCGTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:681336 original size:21 final size:21
Alignment explanation
Indices: 681312--681354 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
681302 TCATATTCGT
* *
681312 TTGAGGGGGTCTCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
*
681333 TTGAATGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
681354 T
1 T
681355 AGCCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.26, G:0.28, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:691234 original size:12 final size:13
Alignment explanation
Indices: 691213--691241 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
691203 ACATACTAAT
691213 ATAATAATAAATA
1 ATAATAATAAATA
691226 ATAAT-ATAAATA
1 ATAATAATAAATA
691238 ATAA
1 ATAA
691242 ACTAAGTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
ATAATAATAAATA
Found at i:700170 original size:89 final size:89
Alignment explanation
Indices: 700019--700196 Score: 356
Period size: 89 Copynumber: 2.0 Consensus size: 89
700009 CACCATAGCC
700019 GCCCACTAACAAGTGTTATTAAGAAGAATTCTAAATTCTTTTGGGGGAAGATCAAGAGAAGTCCT
1 GCCCACTAACAAGTGTTATTAAGAAGAATTCTAAATTCTTTTGGGGGAAGATCAAGAGAAGTCCT
700084 TTAATATAATTAAATATTGTTTAA
66 TTAATATAATTAAATATTGTTTAA
700108 GCCCACTAACAAGTGTTATTAAGAAGAATTCTAAATTCTTTTGGGGGAAGATCAAGAGAAGTCCT
1 GCCCACTAACAAGTGTTATTAAGAAGAATTCTAAATTCTTTTGGGGGAAGATCAAGAGAAGTCCT
700173 TTAATATAATTAAATATTGTTTAA
66 TTAATATAATTAAATATTGTTTAA
700197 TACATGCCCC
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 89 1.00
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (89 bp):
GCCCACTAACAAGTGTTATTAAGAAGAATTCTAAATTCTTTTGGGGGAAGATCAAGAGAAGTCCT
TTAATATAATTAAATATTGTTTAA
Found at i:702118 original size:14 final size:14
Alignment explanation
Indices: 702099--702126 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
702089 CATGCATTGC
702099 ATTTAAATCATCTA
1 ATTTAAATCATCTA
702113 ATTTAAATCATCTA
1 ATTTAAATCATCTA
702127 GTTCATTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (14 bp):
ATTTAAATCATCTA
Found at i:703161 original size:18 final size:18
Alignment explanation
Indices: 703140--703180 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
703130 ATTTAACCTT
703140 ACAACACTATTTGCCACG
1 ACAACACTATTTGCCACG
703158 ACAACACTATTTGCCACG
1 ACAACACTATTTGCCACG
703176 ACAAC
1 ACAAC
703181 GTCATTCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.37, C:0.34, G:0.10, T:0.20
Consensus pattern (18 bp):
ACAACACTATTTGCCACG
Found at i:717323 original size:37 final size:37
Alignment explanation
Indices: 717250--717324 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 37
717240 GTTAAAAAAT
* *
717250 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTAAAAATCATAAA
*
717287 ATTTATATAATTGTT-TTTATAAAATTAAAAAT-ATAAA
1 ATTTATAT-ATT-TTCTTTAAAAAATTAAAAATCATAAA
717324 A
1 A
717325 AGATTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 14 0.42
38 17 0.52
39 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTAAAAATCATAAA
Found at i:719524 original size:15 final size:16
Alignment explanation
Indices: 719497--719533 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
719487 CTTTATTATC
719497 TTATTTCATCTTTCGT
1 TTATTTCATCTTTCGT
*
719513 TTATTT-ATCTTTTGT
1 TTATTTCATCTTTCGT
719528 TTATTT
1 TTATTT
719534 TATTCTAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.14, C:0.11, G:0.05, T:0.70
Consensus pattern (16 bp):
TTATTTCATCTTTCGT
Found at i:719912 original size:21 final size:21
Alignment explanation
Indices: 719886--719942 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
719876 ATTTTTTTTC
719886 AAAAAAACAAAAAAAAAACAA
1 AAAAAAACAAAAAAAAAACAA
719907 AAAAAAACAAAAAAAAAACAA
1 AAAAAAACAAAAAAAAAACAA
* *
719928 AAAAAAGCCAAAAAA
1 AAAAAAACAAAAAAA
719943 GCCAAAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.88, C:0.11, G:0.02, T:0.00
Consensus pattern (21 bp):
AAAAAAACAAAAAAAAAACAA
Found at i:719942 original size:1 final size:1
Alignment explanation
Indices: 719886--719933 Score: 60
Period size: 1 Copynumber: 48.0 Consensus size: 1
719876 ATTTTTTTTC
* * * *
719886 AAAAAAACAAAAAAAAAACAAAAAAAAACAAAAAAAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
719934 GCCAAAAAAG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:719942 original size:11 final size:11
Alignment explanation
Indices: 719886--719933 Score: 89
Period size: 11 Copynumber: 4.5 Consensus size: 11
719876 ATTTTTTTTC
719886 AAAAAAACAAA
1 AAAAAAACAAA
719897 AAAAAAAC-AA
1 AAAAAAACAAA
719907 AAAAAAACAAA
1 AAAAAAACAAA
719918 AAAAAAACAAA
1 AAAAAAACAAA
719929 AAAAA
1 AAAAA
719934 GCCAAAAAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.28
11 26 0.72
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:724222 original size:15 final size:16
Alignment explanation
Indices: 724195--724231 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
724185 CTTTATTATC
724195 TTATTTCATCTTTCGT
1 TTATTTCATCTTTCGT
*
724211 TTATTT-ATCTTTTGT
1 TTATTTCATCTTTCGT
724226 TTATTT
1 TTATTT
724232 TATTCTAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.14, C:0.11, G:0.05, T:0.70
Consensus pattern (16 bp):
TTATTTCATCTTTCGT
Found at i:725812 original size:18 final size:18
Alignment explanation
Indices: 725789--725830 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
725779 ACGTAAACCA
* *
725789 TAAAATTATTGTTTTAAT
1 TAAAATTAATATTTTAAT
*
725807 TAAAATTAATATTTTATT
1 TAAAATTAATATTTTAAT
725825 TAAAAT
1 TAAAAT
725831 GAAAATATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
TAAAATTAATATTTTAAT
Found at i:727145 original size:23 final size:23
Alignment explanation
Indices: 727102--727158 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
727092 TTAGTTTGCA
* *
727102 TAGAATTTTTAGTTTAATATTATT
1 TAGAATTTTTAATTT-ATATTAAT
727126 TAGAATTTTTAATATT-TATTAAT
1 TAGAATTTTTAAT-TTATATTAAT
*
727149 TAGGATTTTT
1 TAGAATTTTT
727159 TGTTTATTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 15 0.52
24 12 0.41
25 2 0.07
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (23 bp):
TAGAATTTTTAATTTATATTAAT
Found at i:730722 original size:2 final size:2
Alignment explanation
Indices: 730715--730746 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
730705 ATATTAAATA
730715 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
730747 TAATTCATAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:730736 original size:28 final size:27
Alignment explanation
Indices: 730647--730736 Score: 67
Period size: 28 Copynumber: 3.1 Consensus size: 27
730637 GTTTAAGAGC
*
730647 ATATGTAAATAATATATGTATA-ATAAT
1 ATAT-TAAATAATATATATATATATAAT
* **
730674 AATAAATAAACTAATATATCATAT-TATAGGG
1 -AT-ATTAAA-TAATATAT-ATATATATA-AT
730705 ATATTAAATAATATATATATATATATAT
1 ATATTAAATAATATATATATATATA-AT
730733 ATAT
1 ATAT
730737 ATATATATAT
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
27 4 0.08
28 22 0.46
29 14 0.29
30 8 0.17
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (27 bp):
ATATTAAATAATATATATATATATAAT
Found at i:742290 original size:45 final size:45
Alignment explanation
Indices: 742226--742314 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 45
742216 TACTGTAATT
* * *
742226 TTATGTTTAAACTCATTTTATGTGAA-CTTGTGATTTTAATCATCG
1 TTATGTTCAAACTCATTTTATAT-AAGCTTGTGATTTCAATCATCG
*
742271 TTATGTTCAAACTCGTTTTATATAAGCTTGTGATTTCAATCATC
1 TTATGTTCAAACTCATTTTATATAAGCTTGTGATTTCAATCATC
742315 TTTGTGTTTG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 2 0.05
45 37 0.95
ACGTcount: A:0.27, C:0.13, G:0.12, T:0.47
Consensus pattern (45 bp):
TTATGTTCAAACTCATTTTATATAAGCTTGTGATTTCAATCATCG
Found at i:742462 original size:35 final size:35
Alignment explanation
Indices: 742421--742493 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
742411 TAAATAACAG
*
742421 AATTTATAGGTTTGTAATACAATTTAAATTTTGCA
1 AATTTATAGGTTTGTAAGACAATTTAAATTTTGCA
* **
742456 AATTTATATGTTTGTAAGACAATTTACGTTTTGCA
1 AATTTATAGGTTTGTAAGACAATTTAAATTTTGCA
742491 AAT
1 AAT
742494 GTTCATTTCT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.45
Consensus pattern (35 bp):
AATTTATAGGTTTGTAAGACAATTTAAATTTTGCA
Found at i:742592 original size:36 final size:36
Alignment explanation
Indices: 742524--742592 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
742514 ATGTACGATT
*
742524 AGAGCAGAATATCATAATTTTATTTTTATTTAAACA
1 AGAGCAGAATATCATAATTTTATTTCTATTTAAACA
*
742560 AGAGCATAATATCAT-ATTTGATATTTCT-TTTAA
1 AGAGCAGAATATCATAATTT--TATTTCTATTTAA
742593 TGAGTAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 4 0.14
36 19 0.66
37 6 0.21
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (36 bp):
AGAGCAGAATATCATAATTTTATTTCTATTTAAACA
Found at i:746906 original size:2 final size:2
Alignment explanation
Indices: 746863--746890 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
746853 TTAAATTTAA
746863 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
746891 TAACTTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:751422 original size:24 final size:24
Alignment explanation
Indices: 751395--751477 Score: 87
Period size: 24 Copynumber: 3.5 Consensus size: 24
751385 AAACATATTT
*
751395 CAGGTCAAGTATCAGATTAGAATC
1 CAGGTCAAGTATCAGATAAGAATC
* *
751419 CAGGTCATGTATCATATAAGAATC
1 CAGGTCAAGTATCAGATAAGAATC
* * *
751443 CATGTCAA-TATTAGATCAGAATC
1 CAGGTCAAGTATCAGATAAGAATC
* *
751466 CATGTCAGGTAT
1 CAGGTCAAGTAT
751478 TATAACAGAA
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
23 19 0.39
24 30 0.61
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (24 bp):
CAGGTCAAGTATCAGATAAGAATC
Found at i:751486 original size:24 final size:23
Alignment explanation
Indices: 751413--751488 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 23
751403 GTATCAGATT
* *
751413 AGAATCCAGGTCATGTATCATATA-
1 AGAATCCATGTCA-GTATTATA-AC
* * *
751437 AGAATCCATGTCAATATTAGATC
1 AGAATCCATGTCAGTATTATAAC
751460 AGAATCCATGTCAGGTATTATAAC
1 AGAATCCATGTCA-GTATTATAAC
751484 AGAAT
1 AGAAT
751489 TCAAATCATA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
23 18 0.43
24 24 0.57
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (23 bp):
AGAATCCATGTCAGTATTATAAC
Found at i:755831 original size:24 final size:24
Alignment explanation
Indices: 755804--755894 Score: 103
Period size: 24 Copynumber: 3.8 Consensus size: 24
755794 CATATTTCAT
* *
755804 GTCAAGTATCATATCAGAATCTAG
1 GTCAAGTATCAGATCAGAATCCAG
* *
755828 GTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAG
*
755852 GTCAA-AATCAGATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* * *
755875 GTCAGGTATCATAACAGAAT
1 GTCAAGTATCAGATCAGAAT
755895 TCAAATCAGA
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
23 20 0.36
24 35 0.64
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAG
Found at i:755865 original size:23 final size:23
Alignment explanation
Indices: 755811--755878 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
755801 CATGTCAAGT
* * **
755811 ATCATATCAGAATCTAGGTCATGT
1 ATCAGATCAGAATCCAGGTCA-AA
*
755835 ATCAGATCAGAATCCATGTCAAA
1 ATCAGATCAGAATCCAGGTCAAA
755858 ATCAGATCAGAATCCAGGTCA
1 ATCAGATCAGAATCCAGGTCA
755879 GGTATCATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
23 20 0.53
24 18 0.47
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.25
Consensus pattern (23 bp):
ATCAGATCAGAATCCAGGTCAAA
Found at i:755871 original size:47 final size:47
Alignment explanation
Indices: 755801--755912 Score: 125
Period size: 47 Copynumber: 2.3 Consensus size: 47
755791 AAACATATTT
* * * * *
755801 CATGTCAAGTATCATATCAGAATCTAGGTCATGTATCAGATCAGAATC
1 CATGTCAA-AATCAGATCAGAATCCAGGTCAGGTATCAGAACAGAATC
* *
755849 CATGTCAAAATCAGATCAGAATCCAGGTCAGGTATCATAACAGAATT
1 CATGTCAAAATCAGATCAGAATCCAGGTCAGGTATCAGAACAGAATC
**
755896 CAAATCAGAAATCAGAT
1 CATGTCA-AAATCAGAT
755913 AAAATATTCA
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
47 37 0.69
48 17 0.31
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.25
Consensus pattern (47 bp):
CATGTCAAAATCAGATCAGAATCCAGGTCAGGTATCAGAACAGAATC
Found at i:767192 original size:87 final size:87
Alignment explanation
Indices: 767029--767194 Score: 208
Period size: 87 Copynumber: 1.9 Consensus size: 87
767019 ATGGAGACGC
* * * * **
767029 AAGACTTCATGTTAATGGCAAACTTATAAAATTTTAAGGAGTAAACATAAAATATTAATAAAAGT
1 AAGACTTCATGTTAAAGGCAAACTTATAAAATTTTAAAGAATAAACATAAAATATCAATAAAAAC
767094 TATAAAAATATATAAAATTTGA
66 TATAAAAATATATAAAATTTGA
* * * *
767116 AAGACTTTATGTTAAAGAGCAAA-TTATAAAATTTTAAAGAATAATCATAAATTATCATTAAAAA
1 AAGACTTCATGTTAAAG-GCAAACTTATAAAATTTTAAAGAATAAACATAAAATATCAATAAAAA
* *
767180 CTATATATATATATA
65 CTATAAAAATATATA
767195 TAATATAATA
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
87 61 0.92
88 5 0.08
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.34
Consensus pattern (87 bp):
AAGACTTCATGTTAAAGGCAAACTTATAAAATTTTAAAGAATAAACATAAAATATCAATAAAAAC
TATAAAAATATATAAAATTTGA
Found at i:767564 original size:14 final size:13
Alignment explanation
Indices: 767550--767598 Score: 53
Period size: 14 Copynumber: 3.6 Consensus size: 13
767540 TATGTGATAG
*
767550 GGTTTATGGTTTA
1 GGTTTAGGGTTTA
767563 GGATTTAGGGTTTA
1 GG-TTTAGGGTTTA
* *
767577 TAGTTTAGGATTTA
1 -GGTTTAGGGTTTA
767591 GGTTTAGG
1 GGTTTAGG
767599 ATTCATAGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
13 9 0.30
14 20 0.67
15 1 0.03
ACGTcount: A:0.20, C:0.00, G:0.33, T:0.47
Consensus pattern (13 bp):
GGTTTAGGGTTTA
Found at i:767571 original size:21 final size:21
Alignment explanation
Indices: 767547--767596 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
767537 AATTATGTGA
*
767547 TAGGGTTTATGGTTTAGGATT
1 TAGGGTTTATAGTTTAGGATT
767568 TAGGGTTTATAGTTTAGGATT
1 TAGGGTTTATAGTTTAGGATT
767589 TA-GGTTTA
1 TAGGGTTTA
767597 GGATTCATAG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 6 0.21
21 22 0.79
ACGTcount: A:0.22, C:0.00, G:0.30, T:0.48
Consensus pattern (21 bp):
TAGGGTTTATAGTTTAGGATT
Found at i:769040 original size:12 final size:12
Alignment explanation
Indices: 769025--769057 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
769015 ACCGAGCTCA
769025 AATTCGAGTTTG
1 AATTCGAGTTTG
*
769037 AATTCGAGCTTG
1 AATTCGAGTTTG
769049 AATT-GAGTT
1 AATTCGAGTT
769058 CGAGCTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 4 0.21
12 15 0.79
ACGTcount: A:0.27, C:0.09, G:0.24, T:0.39
Consensus pattern (12 bp):
AATTCGAGTTTG
Found at i:769059 original size:17 final size:17
Alignment explanation
Indices: 769034--769068 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
769024 AAATTCGAGT
769034 TTGAATTCGAGCTTGAA
1 TTGAATTCGAGCTTGAA
*
769051 TTGAGTTCGAGCTTGAA
1 TTGAATTCGAGCTTGAA
769068 T
1 T
769069 CAAGCTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.26, C:0.11, G:0.26, T:0.37
Consensus pattern (17 bp):
TTGAATTCGAGCTTGAA
Found at i:769088 original size:28 final size:29
Alignment explanation
Indices: 769028--769089 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 29
769018 GAGCTCAAAT
* * * * *
769028 TCGAGTTTGAATTCGAGCTTGAATTGAGT
1 TCGAGCTTGAATTCAAGCTTCAATAGAGC
769057 TCGAGCTTGAA-TCAAGCTTCAATAGAGC
1 TCGAGCTTGAATTCAAGCTTCAATAGAGC
769085 TCGAG
1 TCGAG
769090 TCTCGAGTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 18 0.64
29 10 0.36
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (29 bp):
TCGAGCTTGAATTCAAGCTTCAATAGAGC
Found at i:772578 original size:14 final size:14
Alignment explanation
Indices: 772559--772612 Score: 81
Period size: 14 Copynumber: 3.9 Consensus size: 14
772549 TTGTTAGACT
* *
772559 GAAAATGAATTTTA
1 GAAAATGAATTATG
772573 GAAAATGAATTATG
1 GAAAATGAATTATG
*
772587 GAAAATGAATTACG
1 GAAAATGAATTATG
772601 GAAAATGAATTA
1 GAAAATGAATTA
772613 CATTTTCTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
14 37 1.00
ACGTcount: A:0.52, C:0.02, G:0.19, T:0.28
Consensus pattern (14 bp):
GAAAATGAATTATG
Found at i:776571 original size:29 final size:29
Alignment explanation
Indices: 776513--776575 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
776503 AGCTTCAATA
* *
776513 TGTGTTGATGGATGTTAACTACCATTTTT
1 TGTGTTGATAGATGTTAACTACCATCTTT
* **
776542 TGTGTTGATAGATGTTACCTGTCATCTTT
1 TGTGTTGATAGATGTTAACTACCATCTTT
776571 TGTGT
1 TGTGT
776576 CAATTTTTGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.17, C:0.11, G:0.22, T:0.49
Consensus pattern (29 bp):
TGTGTTGATAGATGTTAACTACCATCTTT
Found at i:776609 original size:41 final size:41
Alignment explanation
Indices: 776538--776626 Score: 108
Period size: 41 Copynumber: 2.2 Consensus size: 41
776528 TAACTACCAT
* * * *
776538 TTTTTGTGTTGATAGATGTTACCTGTCATCTTTTGTGTCAA
1 TTTTTGTGTTGATAGATGTAAACTGCCATCTTTAGTGTCAA
* *
776579 TTTTTGTGTTGAT-GAATGTAAAGTGCCATCTTTAGTGTCAT
1 TTTTTGTGTTGATAG-ATGTAAACTGCCATCTTTAGTGTCAA
776620 TTTTTGT
1 TTTTTGT
776627 ATATGGCATA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
40 1 0.02
41 40 0.98
ACGTcount: A:0.18, C:0.10, G:0.20, T:0.52
Consensus pattern (41 bp):
TTTTTGTGTTGATAGATGTAAACTGCCATCTTTAGTGTCAA
Found at i:776758 original size:72 final size:73
Alignment explanation
Indices: 776615--776761 Score: 242
Period size: 73 Copynumber: 2.0 Consensus size: 73
776605 CATCTTTAGT
*
776615 GTCATTTTTTGTATATGGCATAGTGACTTAGTCAATATGGTATGGTTGCCAAAACCATATACCAC
1 GTCATTTTTTGTATATGGCATAGGGACTTAGTCAATATGGTATGGTTGCCAAAACCATATACCAC
776680 GATATATG
66 GATATATG
* * * *
776688 GTCATTTTTTGTATATGTCATAGGGGCTTAGTTAATATGGTATGGTTGCC-AAACCATATACCAT
1 GTCATTTTTTGTATATGGCATAGGGACTTAGTCAATATGGTATGGTTGCCAAAACCATATACCAC
776752 GATATATG
66 GATATATG
776760 GT
1 GT
776762 AACATTTGGA
Statistics
Matches: 69, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
72 23 0.33
73 46 0.67
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (73 bp):
GTCATTTTTTGTATATGGCATAGGGACTTAGTCAATATGGTATGGTTGCCAAAACCATATACCAC
GATATATG
Found at i:776794 original size:3 final size:3
Alignment explanation
Indices: 776786--776831 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
776776 AATTGATACA
776786 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
776832 GAAACAATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:777068 original size:35 final size:35
Alignment explanation
Indices: 777020--777094 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 35
777010 TCTAAACCCT
777020 AAATTAAAATATTTTAAAATTTAGAGTTTAGAATG
1 AAATTAAAATATTTTAAAATTTAGAGTTTAGAATG
* * * * *
777055 TAATTAAATTATTTTAGAATTTGGGGTTTAGAATG
1 AAATTAAAATATTTTAAAATTTAGAGTTTAGAATG
777090 AAATT
1 AAATT
777095 GAGGATTGTG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.43, C:0.00, G:0.15, T:0.43
Consensus pattern (35 bp):
AAATTAAAATATTTTAAAATTTAGAGTTTAGAATG
Found at i:783497 original size:44 final size:44
Alignment explanation
Indices: 783421--783522 Score: 136
Period size: 44 Copynumber: 2.3 Consensus size: 44
783411 TTGTGCACTG
* *
783421 TGCATCGATACACTATGAAAGTGTACCTATGCA-TCCTTTGAATA
1 TGCATCAATACACTATGAAAGTGCACCTATGCATTCC-TTGAATA
* *
783465 TGCATCAATACACTATGAAGGTGCA-CTGATGCATTCCTTGAATG
1 TGCATCAATACACTATGAAAGTGCACCT-ATGCATTCCTTGAATA
783509 TGCATCAATACACT
1 TGCATCAATACACT
783523 CTGCAGTGTA
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
43 2 0.04
44 47 0.90
45 3 0.06
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (44 bp):
TGCATCAATACACTATGAAAGTGCACCTATGCATTCCTTGAATA
Found at i:785824 original size:65 final size:64
Alignment explanation
Indices: 785695--785850 Score: 190
Period size: 65 Copynumber: 2.4 Consensus size: 64
785685 ACGCCTTAAT
* * * * *
785695 TCGAATGCATTTTGTGTACCGATGCACAGTCATGCTTCGATGCACTCCTGATTTTATTGAAACA
1 TCGAATGCATTTTATGTACCGATGCACAGCCATGCATCGATACACTCCTGATCTTATTGAAACA
* *
785759 TCGAATGCATTTTATGTACCGGTGCACAGACCATGCATCGATACACTCCTGGCTCTT-TTGAAAC
1 TCGAATGCATTTTATGTACCGATGCACAG-CCATGCATCGATACACTCCT-GATCTTATTGAAAC
785823 A
64 A
* *
785824 TCGAATGTA-ATTAGTGTACCGATGCAC
1 TCGAATGCATTTTA-TGTACCGATGCAC
785851 TAGGTCTTAT
Statistics
Matches: 79, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
64 30 0.38
65 45 0.57
66 4 0.05
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.31
Consensus pattern (64 bp):
TCGAATGCATTTTATGTACCGATGCACAGCCATGCATCGATACACTCCTGATCTTATTGAAACA
Found at i:787441 original size:81 final size:81
Alignment explanation
Indices: 786799--787411 Score: 994
Period size: 81 Copynumber: 7.5 Consensus size: 81
786789 AACCTGTCGT
** * * * * * *
786799 TTTTACTCAACATTGTTTAACCGTTCATTTAACTAGCATAATTGGCACATTTATACCAACTGCAC
1 TTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGCACCTTTCTACCAATTGCAC
786864 AGTTAGGCCATTATTC
66 AGTTAGGCCATTATTC
*
786880 TTTTACTCAACGGTATTTAACCGTTCATCTAACTAGCATAATTGGCACCTTTCTACCAATTGCAC
1 TTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGCACCTTTCTACCAATTGCAC
786945 AGTTAGGCCATTATTC
66 AGTTAGGCCATTATTC
* * *
786961 TTTTACTCAACAGTATTTAACCATTCATCTAACTGGCATAATTGGCACCTTTATACCAATTGCAC
1 TTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGCACCTTTCTACCAATTGCAC
787026 AGTTAGGCCATTATTC
66 AGTTAGGCCATTATTC
*
787042 TTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTACCAATTGCAC
1 TTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGCACCTTTCTACCAATTGCAC
787107 AGTTAGGCCATTATTC
66 AGTTAGGCCATTATTC
**
787123 TTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGCATTTTTCTACCAATTGCAC
1 TTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGCACCTTTCTACCAATTGCAC
*
787188 AATTAGGCCATTATTC
66 AGTTAGGCCATTATTC
* * *
787204 TTTTACTCAACGGTATTTAACCGTTGATCTAGCTGGCATAATTGGCACTCTTTTCTACCAATTGT
1 TTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGCAC-C-TTTCTACCAATTGC
787269 ACAGTTAGGCCATTATTC
64 ACAGTTAGGCCATTATTC
787287 TTTTACTCAACGGTATTTAACCGTTCAT-TCAACTGGCATAATTGGCACCTTTCTACCAATTGCA
1 TTTTACTCAACGGTATTTAACCGTTCATCT-AACTGGCATAATTGGCACCTTTCTACCAATTGCA
*
787351 CAGTTAGGCCATTATTA
65 CAGTTAGGCCATTATTC
* *
787368 TTTCACTCAACGGTATTTAACCGTTCATCTAACTGACATAATTG
1 TTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTG
787412 ATACCTTTAT
Statistics
Matches: 497, Mismatches: 31, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
81 420 0.85
82 3 0.01
83 74 0.15
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.37
Consensus pattern (81 bp):
TTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGCACCTTTCTACCAATTGCAC
AGTTAGGCCATTATTC
Found at i:787497 original size:68 final size:68
Alignment explanation
Indices: 787391--787714 Score: 468
Period size: 68 Copynumber: 4.8 Consensus size: 68
787381 TATTTAACCG
* * * * *
787391 TTCATCTAACTGACATAATTGATACCTTTATGTTATAAGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCATAAGCACAGTTAGGCCTCAAAGGCACTTAG
787456 CCT
66 CCT
* *
787459 TTCATCTAACTGGCATAAATGACACATTTCTGTCATAAGCACAGTTAGGCATCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCATAAGCACAGTTAGGCCTCAAAGGCACTTAG
787524 CCT
66 CCT
* * ** *
787527 TTCATCTAACTGGCTTAAATGACACCTTTCTGTCATAAGCACAATTTCGCCTCAAAGACACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCATAAGCACAGTTAGGCCTCAAAGGCACTTAG
787592 CCT
66 CCT
* * * * *
787595 TTCATCTAACTGACATAAATGTCACCTTTCTCTCATAAACACAGTTAGGCCTCAAAGGCACTTAA
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCATAAGCACAGTTAGGCCTCAAAGGCACTTAG
787660 CCT
66 CCT
* * *
787663 TTCATCTAACTGGCTTAGATGACACCTTTTTGTCATAAGCACAGTTAGGCCT
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCATAAGCACAGTTAGGCCT
787715 ATTAATCTTT
Statistics
Matches: 225, Mismatches: 31, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
68 225 1.00
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGACACCTTTCTGTCATAAGCACAGTTAGGCCTCAAAGGCACTTAG
CCT
Found at i:788050 original size:55 final size:53
Alignment explanation
Indices: 787927--788073 Score: 195
Period size: 55 Copynumber: 2.7 Consensus size: 53
787917 CATATATTTT
* *
787927 CCCATACGAACATTCATACACTTGGTATGAATTTCTTAGTTTGCACACATAGTG
1 CCCATACGAA-ATTCATACACTTAGTATGAATTTCTTAGTTTGCACACAAAGTG
* * * *
787981 CCCACACGGAAATTCATACACTTAGCATGAATTTCCTTATTTTTCACACAAAGTG
1 CCCATAC-GAAATTCATACACTTAGTATGAATTT-CTTAGTTTGCACACAAAGTG
*
788036 CCCATACAGAAATTCATACACTTAGTATGAATATCTTA
1 CCCATAC-GAAATTCATACACTTAGTATGAATTTCTTA
788074 CAATTTTTAC
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
54 31 0.38
55 50 0.62
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.32
Consensus pattern (53 bp):
CCCATACGAAATTCATACACTTAGTATGAATTTCTTAGTTTGCACACAAAGTG
Found at i:788577 original size:95 final size:95
Alignment explanation
Indices: 788414--788636 Score: 256
Period size: 95 Copynumber: 2.3 Consensus size: 95
788404 TCTAGCTCTA
* * * * * * * * *
788414 TAGTATCGATACTAC-TACCCTAGTACCGATACTTCTATATTATGGTATCGATAACCCCTTCTGG
1 TAGTATCGATACT-CTTACCATGGTATCGATACTACCATACTATGATACCGATAACCCCTTATGG
788478 TATCGATA-CTGATTTTAGGTTCGATGTTG-T
65 TATCGATATC-GATTTTAGGTTCGATGTTGCT
788508 CTAGTATCGATACTCTTACCATGGTATCGATACTACCATACTATGATACCGA-AACCCCCTTATG
1 -TAGTATCGATACTCTTACCATGGTATCGATACTACCATACTATGATACCGATAA-CCCCTTATG
*
788572 GTATCGATATCGATTTTTGGTTCGATGTTGCT
64 GTATCGATATCGATTTTAGGTTCGATGTTGCT
* * * *
788604 TTGTATTGATACCCTTATCATGGTATCGATACT
1 TAGTATCGATACTCTTACCATGGTATCGATACT
788637 GATTCAATCA
Statistics
Matches: 110, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
94 3 0.03
95 105 0.95
96 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.38
Consensus pattern (95 bp):
TAGTATCGATACTCTTACCATGGTATCGATACTACCATACTATGATACCGATAACCCCTTATGGT
ATCGATATCGATTTTAGGTTCGATGTTGCT
Found at i:790374 original size:3 final size:3
Alignment explanation
Indices: 790366--790424 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
790356 TCCATCTACA
790366 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
790414 AAT AAT AAT AA
1 AAT AAT AAT AA
790425 AACCACATGT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:793115 original size:29 final size:29
Alignment explanation
Indices: 793060--793135 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
793050 TTAACGAGAG
*
793060 AAAACATCATGTATGAAATCGATAATTTT
1 AAAACATCATGTATGAAATCGAAAATTTT
* *
793089 AAAACATTATGTATGAAA-CTGAAAATTTG
1 AAAACATCATGTATGAAATC-GAAAATTTT
* *
793118 ATATACTTCATGTATGAA
1 A-AAACATCATGTATGAA
793136 TGAGATAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
28 1 0.03
29 25 0.64
30 13 0.33
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.34
Consensus pattern (29 bp):
AAAACATCATGTATGAAATCGAAAATTTT
Found at i:793911 original size:18 final size:18
Alignment explanation
Indices: 793888--793949 Score: 76
Period size: 18 Copynumber: 3.5 Consensus size: 18
793878 CATTTCATAT
793888 TTTTCCCTTCATTTCTTC
1 TTTTCCCTTCATTTCTTC
*
793906 TTTTCCCTTTC-TTAAC-T-
1 TTTTCCC-TTCATT-TCTTC
793923 TTTTCCCTTCATTTCTTC
1 TTTTCCCTTCATTTCTTC
793941 TTTTCCCTT
1 TTTTCCCTT
793950 TCTTCACTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
16 4 0.11
17 10 0.27
18 19 0.51
19 4 0.11
ACGTcount: A:0.06, C:0.32, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTCCCTTCATTTCTTC
Found at i:793926 original size:35 final size:35
Alignment explanation
Indices: 793887--793962 Score: 143
Period size: 35 Copynumber: 2.2 Consensus size: 35
793877 TCATTTCATA
793887 TTTTTCCCTTCATTTCTTCTTTTCCCTTTCTTAAC
1 TTTTTCCCTTCATTTCTTCTTTTCCCTTTCTTAAC
*
793922 TTTTTCCCTTCATTTCTTCTTTTCCCTTTCTTCAC
1 TTTTTCCCTTCATTTCTTCTTTTCCCTTTCTTAAC
793957 TTTTTC
1 TTTTTC
793963 TTCTCTATTA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.07, C:0.32, G:0.00, T:0.62
Consensus pattern (35 bp):
TTTTTCCCTTCATTTCTTCTTTTCCCTTTCTTAAC
Found at i:793928 original size:17 final size:16
Alignment explanation
Indices: 793906--793962 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 16
793896 TCATTTCTTC
793906 TTTTCCCTTTCTTAACT
1 TTTTCCCTTTCTT-ACT
*
793923 TTTTCCC-TTCATTTCTT
1 TTTTCCCTTTC-TTAC-T
793940 CTTTTCCCTTTCTTCACT
1 -TTTTCCCTTTCTT-ACT
793958 TTTTC
1 TTTTC
793963 TTCTCTATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
16 4 0.12
17 15 0.45
18 10 0.30
19 4 0.12
ACGTcount: A:0.07, C:0.32, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTCCCTTTCTTACT
Found at i:796303 original size:49 final size:49
Alignment explanation
Indices: 796201--796316 Score: 153
Period size: 49 Copynumber: 2.4 Consensus size: 49
796191 GAGTGTCACC
* * *
796201 TTTTATGCCGAAATGTACCGTTATACATTTAACTTTCATTAGTGGTACC
1 TTTTATGCCGAAATGCACCGTTATACATTTAAATTTCATTAGTGGTACA
* *
796250 TTTTATGCCGAAATGCACCGTTATGCATTTAAATTTCATTATTGGCT-CA
1 TTTTATGCCGAAATGCACCGTTATACATTTAAATTTCATTAGTGG-TACA
* *
796299 TTTTATTCCAAAATGCAC
1 TTTTATGCCGAAATGCAC
796317 TATTATTCAT
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
49 58 0.98
50 1 0.02
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.41
Consensus pattern (49 bp):
TTTTATGCCGAAATGCACCGTTATACATTTAAATTTCATTAGTGGTACA
Found at i:796328 original size:49 final size:49
Alignment explanation
Indices: 796201--796329 Score: 134
Period size: 49 Copynumber: 2.6 Consensus size: 49
796191 GAGTGTCACC
* * * * *
796201 TTTTATGCCGAAATGTACCGTTATACATTTAACTTTCATTAGTGGTACC
1 TTTTATGCCAAAATGCACCATTATACATTTAAATTTCATTAGTGGTACA
* * * *
796250 TTTTATGCCGAAATGCACCGTTATGCATTTAAATTTCATTATTGGCT-CA
1 TTTTATGCCAAAATGCACCATTATACATTTAAATTTCATTAGTGG-TACA
* * *
796299 TTTTATTCCAAAATGCACTATTATTCATTTA
1 TTTTATGCCAAAATGCACCATTATACATTTA
796330 TTTTAGCACC
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
49 68 0.99
50 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.43
Consensus pattern (49 bp):
TTTTATGCCAAAATGCACCATTATACATTTAAATTTCATTAGTGGTACA
Found at i:798328 original size:89 final size:89
Alignment explanation
Indices: 798227--798397 Score: 324
Period size: 89 Copynumber: 1.9 Consensus size: 89
798217 CGATCGGAGA
*
798227 CTATCTTTAGATTATCTTGGAAAACTATCACTTTCTCTTCCATTTCTTTAACCAAATATGGACCA
1 CTATCTTTAGATTATCTTGGAAAACTATCACTTTCTCTTCCATTTATTTAACCAAATATGGACCA
798292 ACTAGGTCTCGATCTTTTCAGAGG
66 ACTAGGTCTCGATCTTTTCAGAGG
*
798316 CTATCTTTAGATTATCTTGGAAAACTATCACTTTCTCTTCCATTTATTTAACCAAATTTGGACCA
1 CTATCTTTAGATTATCTTGGAAAACTATCACTTTCTCTTCCATTTATTTAACCAAATATGGACCA
798381 ACTAGGTCTCGATCTTT
66 ACTAGGTCTCGATCTTT
798398 GAGTTCAAAC
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 80 1.00
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.40
Consensus pattern (89 bp):
CTATCTTTAGATTATCTTGGAAAACTATCACTTTCTCTTCCATTTATTTAACCAAATATGGACCA
ACTAGGTCTCGATCTTTTCAGAGG
Found at i:803653 original size:1 final size:1
Alignment explanation
Indices: 803647--803692 Score: 74
Period size: 1 Copynumber: 46.0 Consensus size: 1
803637 AGAAGAAAGC
* *
803647 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
803693 GAAATTTGCA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.96, C:0.00, G:0.04, T:0.00
Consensus pattern (1 bp):
A
Found at i:816527 original size:22 final size:22
Alignment explanation
Indices: 816496--816539 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
816486 AAAATATGAT
816496 ATGAACAATGCCATGAACAGTA
1 ATGAACAATGCCATGAACAGTA
*
816518 ATGAATAATGCCATGAACAGTA
1 ATGAACAATGCCATGAACAGTA
816540 CTACAGTGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.45, C:0.16, G:0.18, T:0.20
Consensus pattern (22 bp):
ATGAACAATGCCATGAACAGTA
Found at i:817305 original size:18 final size:18
Alignment explanation
Indices: 817282--817316 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
817272 ACTGAATATT
*
817282 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
817300 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
817317 CCTTAAGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.34, G:0.20, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:817424 original size:23 final size:23
Alignment explanation
Indices: 817398--817441 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
817388 ATTATATATA
817398 TGTCCCGAAGGACCACGTAGAAT
1 TGTCCCGAAGGACCACGTAGAAT
* *
817421 TGTCTCGAAGGACCGCGTAGA
1 TGTCCCGAAGGACCACGTAGA
817442 CCCTCGACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.25, G:0.30, T:0.18
Consensus pattern (23 bp):
TGTCCCGAAGGACCACGTAGAAT
Found at i:819785 original size:21 final size:21
Alignment explanation
Indices: 819759--819804 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
819749 CCTGGAAGAG
**
819759 AAGCCCCTAATTTGTAAACTC
1 AAGCCCCTAATTTACAAACTC
819780 AAGCCCCTAATTTACAAACTC
1 AAGCCCCTAATTTACAAACTC
819801 AAGC
1 AAGC
819805 AAATATTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.37, C:0.30, G:0.09, T:0.24
Consensus pattern (21 bp):
AAGCCCCTAATTTACAAACTC
Done.